Additional domains for each of the IRAK, R. irregularis, and PknB-related pseudokinase families were initially identified using NCBI’s Batch Web CD-Search Tool against the Conserved Domain Database with an expected value threshold of 0.01 and a maximum of 500 hits per CD-search (133, 134). TM helices were identified using TMHMM 2.0 (135) and the Phobius web server (136). TM helices were annotated as such only if both TMHMM and Phobius predicted the same TM helix region within a 10-residue margin. We verified kinase domain hits using our manually curated protein kinase profiles and removed any overlapping domain predictions.

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